May 2022 - Comp-neuro - lists.cnsorg.org

New 4-years PostDoc position in "Explainable Machine / Deep Learning in Translational Psychiatry" at Charité - Universitätsmedizin Berlin, Germany

by Kerstin Ritter

Dear all, John-Dylan Haynes and I offer a new PostDoc position in the field of "Explainable Machine Learning / Deep Learning in Clinical Neuroimaging and Translational Psychiatry" at Charité - Universitätsmedizin Berlin, Germany (see advertisement below) - please feel free to forward the advertisement to people who may be interested! Thanks a lot! Best wishes, Kerstin Ritter ______________________________________________________________ Explainable Machine Learning / Deep Learning in Clinical Neuroimaging and Translational Psychiatry PostDoc position (starting date: July/August 2022, up to 4 years; 100 %) at Charité - Universitätsmedizin (Berlin, Germany) At Charité - Universitätsmedizin Berlin and the Bernstein Center for Computational Neuroscience, we are looking for a motivated and highly qualified PostDoc for methods development at the intersection of explainable machine learning / deep learning and clinical neuroimaging / translational psychiatry. The position will be located in the research groups of Ass. Prof. Kerstin Ritter and Prof. John-Dylan Haynes at Charité Berlin. The main task will be to predict response to cognitive-behavioral psychotherapy in retrospective data and a prospective cohort of patients with internalizing disorders including depression and anxiety from a complex, multimodal data set comprising tabular data as well as imaging data (e.g., clinical data, smartphone data, EEG, structural and functional MRI data). An additional task will be to contribute to the organization and maintenance of the prospective cohort. This study will be one of several projects in the newly established Research Unit 5187 "Precision Psychotherapy" (headed by Prof. Ulrike Lüken). Please see also the job advertisement: https://www.charite.de/service/stellenangebot/angebot/detailinfo/dm11822b_r… Requirements for the Postdoc: - Excellent degree in relevant field (e.g. computer science, mathematics, physics, psychology, computational neuroscience or related). - Excellent methodological skills (esp. machine learning, deep learning, explainable AI, medical image analysis) - Excellent programming skills in python - Excellent writing and communication skills (in English) - Strong interest in neuroscientific and psychiatric research Please send your application (motivation+CV+references) in one pdf-file (in English or German) asap to: Ass. Prof. Dr. rer. nat. Kerstin Ritter Charité - Universitätsmedizin Berlin Department of Psychiatry and Psychotherapy Bernstein Center for Computational Neuroscience Sauerbruchweg 4, Charitéplatz 1, 10117 Berlin E-Mail: kerstin.ritter(a)charite.de Webpage: https://psychiatrie-psychotherapie.charite.de/en/research/translation_and_n… ______________________________________________________________

May 19, 2022

Junior Chair position in Computational Neuroscience, Marseille, France

by Sylvain Takerkart

Aix-Marseille Université (AMU) is opening a Junior Chair in Computational Neuroscience, a new tenured-track path at French Universities. The position is open at Junior Professor level (level of experience 3-10 years after PhD) and is supported with a start-up package of 470K€, including the salary for the Junior Professor. After 3-5 years, depending upon the scientific achievements, the Chair should lead to a permanent Faculty position at the Professor level (PR2). * Starting date: Sept-Dec 2022 (not flexible) * teaching is about 60h/year (negotiable) in Computational neurosciences * deadline of application June 8th * Inquiries and further information can be sent directly to both Dr Guillaume Masson (Director INT:guillaume.masson@univ-amu.fr <mailto:guillaume.masson@univ-amu.fr>) and Dr Viktor Jirsa (Director INS:viktor.jirsa@univ-amu.fr <mailto:viktor.jirsa@univ-amu.fr>) More info (in French, then in English) at https://www.galaxie.enseignementsup-recherche.gouv.fr/ensup/ListesPostesPub… <https://www.galaxie.enseignementsup-recherche.gouv.fr/ensup/ListesPostesPub…> Please circulate! -- Sylvain Takerkart Institut des Neurosciences de la Timone (INT) UMR 7289 CNRS-AMU Marseille, France tél: +33 (0)4 91 324 007 http://www.int.univ-amu.fr/_TAKERKART-Sylvain_?lang=en

May 19, 2022

Call for papers for the 5th international workshop on machine learning in clinical neuroimaging

by MLCN Workshop

Dear Colleagues, Please find below the call for papers for the International Workshop of Machine Learning in Clinical Neuroimaging (MLCN) which is held on *the 18th of September 2022 at MICCAI 2022, Singapore*. We welcome contributions to novel machine learning methods and their applications to clinical neuroimaging data. The submission deadline is *25 June 2022*, and all MLCN accepted papers will be eligible for the best paper award of 500 USD. Top accepted papers will be invited to submit an extended version to the MELBA journal. For more information, please visit https://mlcnws.com/call-for-papers/*.* Best wishes, The MLCN 2022 steering and organizing committees Christos Davatzikos, Andre Marquand, Jonas Richiardi, Emma Robinson Ahmed Abdulkadir, Nicha C. Dvornek, Mohamad Habes, Seyed Mostafa Kia, Vinod Kumar, Thomas Wolfers *Call for Papers* The International Workshop of Machine Learning in Clinical Neuroimaging (MLCN 2022 <https://mlcnws.com/>), a satellite event of MICCAI (MICCAI 2022 <https://conferences.miccai.org/2022/en/>), calls for original papers in the field of clinical neuroimaging data analysis with machine learning. The two tracks of the workshop include methodological innovations as well as clinical applications. This highly interdisciplinary topic provides an excellent platform to connect researchers of varying disciplines and to collectively advance the field in multiple directions. In the *machine learning* track, we seek novel contributions that address current methodological gaps in analyzing high-dimensional, longitudinal, and heterogeneous clinical neuroscientific data using stable, scalable, and interpretable machine learning models. Topics of interest include but are not limited to: · Big data · Spatio-temporal brain data analysis · Structural data analysis · Graph theory and complex network analysis · Longitudinal data analysis · Model stability and interpretability · Model scalability in large neuroimaging datasets · Multi-source data integration and multi-view learning · Multi-site data analysis, from preprocessing to modeling · Domain adaptation, data harmonization, and transfer learning in neuroimaging · Unsupervised methods for stratifying brain disorders · Deep learning in clinical neuroimaging · Model uncertainty in clinical predictions · … In the *clinical neuroimaging *track*,* the applications of existing machine learning algorithms are evaluated to move towards precision medicine for complex brain disorders. The discovery of biological markers in medicine is an important challenge across different fields and various experimental procedures and designs are used to detect biological signatures that can be utilized for improvement in diagnostic, treatment, or for other beneficial ends. However, for most complex brain disorders, we do not have reliable biomarkers today. The application of advanced machine learning methods may help to reach this goal. Therefore, we invite the community to submit conference contributions on machine learning approaches with the goal to improve our understanding of complex brain disorders, moving the field closer to precision medicine. Topics of interest include but are not limited to: · Biomarker discovery · Refinement of nosology and diagnostics · Biological validation of clinical syndromes · Treatment outcome prediction · Course prediction · Analysis of wearable sensors · Neurogenetics and brain imaging genetics · Mechanistic modeling · Brain aging · The presentation of clinical neuroimaging databases to stimulate developments in machine learning · … ------------------------------ *Submission Process:* The workshop seeks high-quality, original, and unpublished work that addresses one or more challenges described above. Papers should be submitted electronically in Springer Lecture Notes in Computer Science (LCNS) style (see this link <https://conferences.miccai.org/2022/en/PAPER-SUBMISSION-AND-REBUTTAL-GUIDEL…> for detailed author guidelines) using the CMT system here <https://cmt3.research.microsoft.com/MLCN2022>. The page limit is 8-pages (text, figures, and tables) plus up to 2-pages of references. We review the submissions in a double-blind process. Please make sure that your submission is anonymous. Accepted papers will be published in a joint proceeding with the MICCAI 2022 conference. ------------------------------ *MLCN Special Issue at the MELBA journal:* We will invite the top accepted papers to submit an extended version of their contribution to the MLCN special issue at the Journal of Machine Learning for Biomedical Imaging (MELBA) <https://www.melba-journal.org/>. The invited papers will go through an independent review process by the journal. *Error! Filename not specified.* <https://www.melba-journal.org/> ------------------------------ *Donders Best Paper Award:* The MLCN’s best paper award is sponsored by Donders Institute <https://www.ru.nl/donders/>. All MLCN accepted papers will be eligible for the best paper award. The recipient of the award will be chosen by the MLCN scientific committee based on the scientific quality, novelty, and clarity of contributions. The winner will be announced at the end of the workshop and will receive a 500 USD honorarium. ------------------------------ *Important Dates:* · Paper submission deadline: June 25, 2022 · Notification of Acceptance: July 23, 2022 · Camera-ready Submission: Aug 6, 2022 · Workshop Date: September 18, 2022

May 18, 2022

Final reminder: 9th Baltic-Nordic Summer School on Neuroinformatics (BNNI 2022)

by Daniel Wójcik

*Deadline this Sunday.* Apologies for cross-posting. Please distribute.* ------------------------------------------------------- 9th Baltic-Nordic Summer School on Neuroinformatics (BNNI 2022)* /Understanding neurons, cognition and behavior// //through neuroinformatics and artificial intelligence/ *Place* The Campus of the 600th Anniversary of the Jagiellonian University Revival Faculty of Management and Social Communication / Faculty of Mathematics and Computer Science Krakow, Poland *Time:* July 4-8, 2022 *More information and applications at* http://bionn.matinf.uj.edu.pl/events/bnni2022/ * **Important dates* *22 May 2022 Application deadline* 31 May 2022 Acceptance notification 4-8 July 2022 Summer School *We invite advanced master students, doctoral students, and postdoctoral researchers to participate in the BNNI 2022 to be held at Jagiellonian University in Kraków.* The course is interdisciplinary and covers modeling at different levels of organization of the brain as well as elements of machine learning. The course combines lectures, tutorials and computer exercises for computational modeling and analysis of brain functions at multiple physiological and anatomical scales. The summer school will follow the series of the Baltic-Nordic Courses on Neuroinformatics (BNNI 2013 in Kaunas, BNNI 2014 in Tampere, BNNI 2015 in Tartu, BNNI 2016 in Warsaw, BNNI 2017 in Kaunas, BNNI 2018 in Ventspils, BNNI 2019 <https://bnni.lsmuni.lt/bnni2019/en> in Frankfurt, BNNI 2021 <https://www.humanbrainproject.eu/en/education/BNNI2021/> online). The *target audience* of the course will be advanced master students, doctoral students and postdoctoral researchers in natural science, including physics, chemistry, mathematics, computer science, informatics and information technology, and similar who would like to get an introduction to neuroinformatics and computational neuroscience. Advanced master students, doctoral students and postdoctoral researchers in neuroscience and psychology with strong interest in computer science, data analysis and mathematics, and some educational and/or research background in quantitative science are also encouraged to apply. *The school will be in hybrid format with up to 40 in-person places.* *Faculty includes* Hermann Cuntz, Ernst Strüngmann Institute (ESI) for Neuroscience, Frankfurt, Germany Gaute Einevoll, Norwegian University of Life Sciences and University of Oslo, Norway Boris Gutkin, Ecole Normale Superieure, Paris, France Adam Hamed, Nencki Institute of Experimental Biology, Warsaw, Poland Gabriela Izowit, Jagiellonian University, Kraków, Poland Dieter Jaeger, Emory University Peter Jedlicka, Faculty of Medicine, Justus-Liebig-University and NeuroScience Center, Goethe-University, Germany Ewelina Knapska, Nencki Institute of Experimental Biology, Warsaw, Poland Jan Fousek, Aix-Marseille University, France Marja-Leena Linne, Tampere University of Technology, Finland Jan Rodriguez Parkitna, Maj Institute of Pharmacology, Kraków, Poland Igor Podolak, Jagiellonian University, Kraków, Poland Arnd Roth, University College London, UK Ausra Saudargiene, Lithuanian University of Health Sciences, Kaunas, Lithuania Dirk Schubert, Radboud University, Netherlands Wolfram Schultz, University of Cambridge, UK Eleni Vasilaki, University of Sheffield, Sheffield, United Kingdom Daniel Wójcik, Nencki Institute of Experimental Biology, Warsaw & Jagiellonian University, Kraków, Poland Mirosław Wyczesany, Jagiellonian University, Kraków, Poland Friedemann Zenke, Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland *Venue* The lectures will be held at the Faculty of Management and Social Communication and the computer classes in the Faculty of Mathematics and Computer Science at the new The Campus of the 600th Anniversary of the Jagiellonian University Revival. The two buildings are next to each other and connected to Kraków center by multiple tram and bus lines. *Registration fee* In person attendance: 100 EUR; covers lunches, coffee breaks and special dinner during the school. Online attendance: 10 EUR; covers transmission costs. The organizers will provide teaching, meals and coffee during the course. The participants are expected to cover their travel and health insurance expenses as well as lodging. We will provide advise with inexpensive lodging for all the students. *Available support* We will award scholarships to 20 in-person participants from outside of Poland. The scholarship (over 4000 PLN before tax) comes with a fee waiver and should be enough to cover travel and lodging during the school. *Funding *The course is supported by the SPINAKER program financed by the National Agency for Academic Exchange (NAWA) in Poland.* * We are looking forward to welcome you at the BNNI 2022 in Kraków in July!

May 18, 2022

Date change: Susan Goldin-Meadow speaking on June 1 in Developing Minds global online lecture series

by Jochen Triesch

Dear colleagues, On June 1, the Developing Minds global online lecture series will feature Susan Goldin-Meadow, Dept. of Psychology, U. of Chicago, USA. : "The Mind Hidden in Our Hands“ https://sites.google.com/view/developing-minds-series/home The talk had to be postponed from the originally planned date of May 18. The live event will take place via zoom at: 08:00 CDT (Central Daylight Time) 13:00 UTC (Universal Coordinated Time) 15:00 CEST (Central European Summer Time) 22:00 JST (Japan Standard Time) To participate please register here: https://sites.google.com/view/developing-minds-series/home Abstract Gesture is versatile in form and function. Under certain circumstances, gesture can substitute for speech, and when it does, it embodies the properties of language that children themselves bring to language learning, and underscores the resilience of language itself. Under other circumstances, gesture can form a fully integrated system with speech. When it does, it both predicts and promotes learning, and underscores the resilience of gesture in thinking. Together, these lines of research show how much of our minds is hidden in our hands. Bio Susan Goldin-Meadow is the Beardsley Ruml Distinguished Service Professor in the Departments of Psychology and Comparative Human Development at the University of Chicago. Her research focuses on the most basic building blocks of language and thought as they are developed in early childhood. Specifically, she is interested in uncovering linguistic components that are so basic they will arise in a child’s communication system even if the child has limited access to outside linguistic input. Professor Goldin-Meadow’s research has also generated more broadly applicable insights into how the spontaneous gestures that learners produce can reveal their readiness to learn language, math, and scientific concepts. Professor Goldin-Meadow is the founding Editor of Language Learning and Development, and has been president of the International Society for Gesture Studies, president of the Cognitive Development Society, chair of the Cognitive Science Society, and president of the Association for Psychological Society. She is the recipient of a Guggenheim Fellowship, received the William James award for lifetime achievement in basic research from APS, was elected to the American Academy for Arts and Science in 2005, and the National Academy of Sciences in 2020. Web: https://psychology.uchicago.edu/directory/susan-goldin-meadow The talk will also be recored and the recording made available via the web page: https://sites.google.com/view/developing-minds-series/home Stay healthy, Jochen Triesch -- Prof. Dr. Jochen Triesch Johanna Quandt Chair for Theoretical Life Sciences Frankfurt Institute for Advanced Studies and Goethe University Frankfurt http://fias.uni-frankfurt.de/~triesch/ Tel: +49 (0)69 798-47531 Fax: +49 (0)69 798-47611

May 17, 2022

Submissions for trainee talks at CCNSv3 (June 6-7 on Crowdcast) are open

by Scott Rich

The third edition of the CCNS meeting is less than three weeks away! The program is being updated daily at ccnsmeeting.ca. Three of our keynote speakers are confirmed: Drs. Gaute Einevoll, Viktor Jirsa, and Cendri Hutcherson. Other confirmed speakers include Drs. Willy Wong, Steven Prescott, Carmen Canavier, Kelly Shen, and Casper Hesp. To register for the meeting, head over to https://www.crowdcast.io/e/ccnsv3/register. We are also still accepting submissions for Trainee Talks at https://docs.google.com/forms/d/e/1FAIpQLSdF1cFvCOKFuwYJf_e1QpLZaxnANE-xjuG…. Submissions received before May 23 will receive full consideration. We look forward to seeing you at CCNSv3! Sincerely, Scott Rich (on behalf of the organizing committee)

May 17, 2022

New publication from the INCF Infrastructure Committee

by INCF

The INCF Infrastructure Committee’s “Recommendations for repositories and science gateways from a neuroscience perspective” <https://www.nature.com/articles/s41597-022-01334-1> has been published today, May 16, as a Comment in Scientific Data <https://www.nature.com/sdata/>. The project, initiated by the INCF Infrastructure Committee, aimed to develop an inclusive set of criteria that could apply to a wide and diverse range of digital services, including repositories, science gateways, data, and software. “We set out to develop criteria that were specific to neuroscience, but we realized during the process that our end result would be applicable to other data-heavy disciplines as well”, says Malin Sandström, coordinator for the Infrastructure Committee. “When you look at the problem closely, it turns out that many of the criteria have to do with best practices for how a service is run and governed, rather than with which types of data and other content it contains”. The work began in October 2020. A draft version <https://www.incf.org/criteria-checklist> was presented to the community at the INCF Assembly in April 2021, in a workshop <https://f1000research.com/documents/10-1026> with representatives from organizations engaged in similar projects, including FAIRSharing, FORCE11, and the Coalition of Open Access Repositories (COAR). A public first version of the criteria checklist was made available on the INCF portal <https://www.incf.org/criteria-checklist> in late 2021. With these criteria, INCF wants to help neuroscience researchers and students choose good services for their specific use cases and help service providers make good and future-proof decisions for setup and operations. Former Chair Wojtek Goscinski, now Chief Executive Officer at the Australian National Imaging Facility, explains: “Data repositories and scientific gateways are critical, but often underappreciated, components in the scientific workflow. It’s important that researchers can navigate the digital landscape to find the services that they need and to understand which services are fit-for-purpose. Likewise, repositories and gateways have increasing obligations to their users”. The recommendations published in the Comment are intended to guide users through the reasoning and considerations that went into the criteria development process. Read more: Workshop report <https://f1000research.com/documents/10-1026> Public first version criteria <https://www.incf.org/criteria-checklist> Blog post <https://incf.org/blog/incf-infrastructure-committee-recommendations-publish…>

May 16, 2022

Postdoc positions in modeling/analysis for understanding sleep

by Geoffrey Goodhill

POSTDOC POSITIONS IN MODELING/ANALYSIS FOR UNDERSTANDING SLEEP OVERVIEW. A new NIH-funded collaboration between David Prober (Caltech), Thai Truong (USC) and Geoff Goodhill (Washington University in St Louis) aims to gain new insight into the neural circuits underlying sleep, through a combination of whole-brain neural recordings in zebrafish and theoretical/computational modeling. The Goodhill lab is now looking for 2 postdocs for the modeling and computational analysis components. PROJECT DETAILS. Using novel 2-photon imaging technologies Prober and Truong will record from the entire larval zebrafish brain at single-neuron resolution continuously for long periods of time, examining neural circuit activity during normal day-night cycles and in response to genetic and pharmacological perturbations. The Goodhill lab will analyze the resulting huge datasets using a variety of sophisticated computational approaches, and use these results to build new theoretical models that reveal how neural circuits interact to govern sleep. Theoretical and experimental work will be intimitely linked. APPLICANT PROFILE. Applicants for the positions in the Goodhill lab should have a strong background in mathematics/theory/computation applied to biological problems. Experience in modeling sleep processes is desirable but not required. LAB ENVIRONMENT. The Goodhill lab is an interdisciplinary environment of students and postdocs from a diverse array of backgrounds including neuroscience, mathematics, physics and engineering, working together on understanding neural circuit computation, particularly relating to neural development. The lab both performs its own behavioral and neural imaging experiments with larval zebrafish, and collaborates on the analysis of data generated elsewhere. UNIVERSITY ENVIRONMENT. Washington University in St Louis is ranked in the top 10 institutions globally for Neuroscience and Behavior, and offers an outstanding intellectual environment for research in neuroscience. In 2023 the Goodhill lab will move along with over 100 other labs into Washington University's new start-of-the-art 600,000 sq ft Neuroscience Research Building (https://neuroscience.wustl.edu/research/neuroscience-building) For more information about St Louis see https://explorestlouis.com. To apply please send a detailed CV and cover letter explaining your interest in the positions to g.goodhill(a)wustl.edu. Review of applications will continue until the positions are filled. Professor Geoffrey J Goodhill Departments of Developmental Biology, Neuroscience, Biomedical Engineering, and Electrical and Systems Engineering Washington University in St Louis St Louis, MO 63110 https://neuroscience.wustl.edu/people/geoffrey-goodhill-phd Email: g.goodhill(a)wustl.edu

May 15, 2022

Research Fellow / Postdoc positions in Complex Networks and Brain Dynamics, Prague, Czech Republic

by Magda Pokorna

*Research Fellow / Postdoc positions in Complex Networks and Brain Dynamics is available in Prague, Czech Republic:* We are looking for new team members to join the _Complex Networks and Brain Dynamics group <http://cobra.cs.cas.cz/>_to work on its interdisciplinary projects. The group is part of the *Department of Complex Systems, Institute of Computer Science of the Czech Academy of Sciences - based in Prague, Czech Republic,*_https://www.cs.cas.cz/ <https://www.cs.cas.cz/>_. We focus on the development and application of methods of analysis and modelling of real-world complex networked systems, with particular interest in the structure and dynamics of human brain function. Our main research areas are neuroimaging data analysis (fMRI & EEG, iEEG, anatomical and diffusion MRI), brain dynamics modelling, causality and information flow inference, nonlinearity and nonstationarity, graph theory, machine learning and multivariate statistics; with applications in neuroscience, climate research, economics and general communication networks. More information about the group at _http://cobra.cs.cas.cz/ <http://cobra.cs.cas.cz/>_. **Applications will be reviewed on a rolling basis with a first cut-off point on June 30, 2022.** For more information and application see https://www.cs.cas.cz/job-offer/research-fellow-postdoc-position-Hlinka1-20… Do not hesitate to contact the principal investigator for informal inquiries concerning the position: Ing. Mgr. Jaroslav Hlinka, Ph.D., hlinka(a)cs.cas.cz, Web: http://cs.cas.cz/hlinka. Institute of Computer Science Czech Academy of Sciences Pod Vodarenskou vezi 2 Prague 8, 182 07, Czech Republic https://www.cs.cas.cz/

May 12, 2022

Postdoc / Junior Scientist in Multimodal Neuroimaging Machine Learning, Prague, Czech Republic

by Magda Pokorna

Postdoctoral / Junior Scientistposition in Multimodal Neuroimaging Machine Learning is available in Prague, Czech Republic: A postdoc or junior scientistposition is available to join the _Complex Networks and Brain Dynamics group <http://cobra.cs.cas.cz/>_for the project: /“Predicting functional outcome in schizophrenia from multimodal neuroimaging and clinical data“/funded by the Czech Health Research Council.The project involves the development of tools to predict the functional outcome of schizophrenia from multimodal neuroimaging, clinical and cognitive measurements taken early after disease onset. To overcome limitations due to high dimensionality of data, we combine robust machine-learning tools, data-driven feature selection and theory-based brain network priors.The project is carried out in collaboration with the National Institute of Mental Health, using its unique large rich imaging, cognitive and biochemical data of early stage schizophrenia patients. **Applications will be reviewed on a rolling basis with a first cut-off point on June 30, 2022.** For more information and application see https://www.cs.cas.cz/job-offer/postdoctoral-junior-scientist-position-Hlin… Do not hesitate to contact the principal investigator for informal inquiries concerning the position: Ing. Mgr. Jaroslav Hlinka, Ph.D., hlinka(a)cs.cas.cz, Web: http://cs.cas.cz/hlinka. Institute of Computer Science Czech Academy of Sciences Pod Vodarenskou vezi 2 Prague 8, 182 07, Czech Republic https://www.cs.cas.cz/

May 12, 2022